I've had poor luck with such simple equilibrations.
We usually do a series of MD runs, with equilibration of water and all built
atoms first, then restraints on fewer atoms (first all heavy, then backbone
only) and heating /minimization steps. I don't heat from 0, I have had bad
experiences and always start MD at 200K or so and heat from there. we only
use positional restraints.
On Tue, May 31, 2011 at 9:03 AM, Oliver Kuhn <oak.amber.googlemail.com>wrote:
> Dear Ambers,
>
> I'm doing standard MD simulations on HIV protease (as many of you might
> know
> ;) and I observe angular oscillations (that might damp after some
> nanoseconds).
>
> -> That means, I observe oscillations in the sum of angle energies of the
> complex (see attached plot - 100ps blockwise averages) (in 21 independent
> simulations)
>
> My protocol involves minimization of water and hydrogens first, then
> minimization of the whole system (no restraints), then heatup phase 50ps
> (no
> restraints).
>
> Not so important:
> Are there any obvious improvements that can be suggested for minimization?
> Does anybody have experienced for example that its better to relax
> side-chains before relaxing the whole system including backbone or
> something
> like this.
>
> Important:
> Now I want to use restraints during heatup to guide the molecule to
> equilibrium and release it there.
> My idea would be to use phi psi backbone torsional restraints. Is this ok
> or
> is there something wrong with this idea?
> I want to gradually reduce the restraints during 50ps heatup.
> What initial force constant should I use?
> Is 50 ps enough for such a procedure?
> Should I use a different type of restraint?
>
> Thanks for any suggestions
> Regards,
> Oliver
>
>
> --
> Oliver Kuhn, Department of Bioinformatics,
> Center for Medical Biotechnology, University of Duisburg-Essen,
> Universitätsstr. 1-5, 45141 Essen, Germany
> phone +49 201 183-3121, oliver.kuhn.uni-due.de
>
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Received on Tue May 31 2011 - 12:00:02 PDT
